Nyaaaah.
BioWare did confirm that this was the end to Shepard part of the Mass Effect stories, but that the ME Universe will live on and flourish.

What everyone seems to forget is that during the course of 3 games you've had but one end goal: To Destroy the Reapers.
In the end the Reapers realize that Shepard won't stop do achieve this, so they give him other options.

Also, I thought from the beginning that Starchild had created the Reapers in fear of something bigger and darker of which he refers to as "The Machine Devils"... but the Leviathan DLC completley wrecked that theory.

But when you look at the ending of both Synthesis and Control, Shepard's eyes turn into the same robotic eyes that Saren and the Illusive Man had.
The eyes turning to that is the final sign of complete Indoctrination.